Genomic implications of low effective population size in non-model mammalian species

Peers, Jessica (2025) Genomic implications of low effective population size in non-model mammalian species. Doctoral thesis, University of East Anglia.

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Abstract

Small populations, particularly those that have experienced severe genetic bottlenecks, suffer from increased inbreeding and accumulations of deleterious mutations across the genome. Although many studies have examined the impact of these mutations in protein-coding genes, the effects of low effective population size (Ne) on the non-coding genome remain largely unknown, as most non-coding research to date focuses on model species. In this thesis, I investigate the effects of low Ne in a non-model mammalian species, the cheetah (Acinonyx jubatus), considering both the coding and non-coding genome. I identify premature termination codons in fertility-related genes that are shared across multiple unrelated cheetahs. I then evaluate the application of machine learning methods to annotate the non-coding genome of non-model species, negating the requirement for bespoke experimental data and expanding our ability to study species that lack such resources. Finally, I analyse inbreeding and mutation load in both captive and wild cheetahs and identify putative deleterious mutations across the genome in fertility-related genes. Overall, this thesis contributes to our understanding of the impacts of low Ne across the genome and provides a framework to study any non-model species, accelerating research into the non-coding genome and its applications in conservation.

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Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Kitty Laine
Date Deposited:	06 May 2026 11:05
Last Modified:	06 May 2026 11:05
URI:	https://ueaeprints.uea.ac.uk/id/eprint/102912
DOI:

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